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- PDB-4hll: Crystal structure of Artificial ankyrin repeat protein_Ank(GAG)1D4 -

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Basic information

Entry
Database: PDB / ID: 4hll
TitleCrystal structure of Artificial ankyrin repeat protein_Ank(GAG)1D4
ComponentsAnkyrin(GAG)1D4
KeywordsPROTEIN BINDING / Ankyrin repeats
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChuankhayan, P. / Nangola, S. / Minard, P. / Boulanger, P. / Hong, S.S. / Tayapiwatana, C. / Chen, C.-J.
CitationJournal: To be Published
Title: Identification of Gag bioactive determinants specific to designed ankyrin and interfering in HIV-1 assembly
Authors: Chuankhayan, P. / Nangola, S. / Minard, P. / Boulanger, P. / Hong, S.S. / Tayapiwatana, C. / Chen, C.-J.
History
DepositionOct 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ankyrin(GAG)1D4


Theoretical massNumber of molelcules
Total (without water)18,7771
Polymers18,7771
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.240, 29.016, 50.044
Angle α, β, γ (deg.)90.00, 98.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ankyrin(GAG)1D4


Mass: 18777.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Description: THE SEQUENCE DERIVED FROM A PHAGE-DISPLAYED LIBRARY PRODUCED FOR E.COLI.
Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4]
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 400, 5% PEG 3000, 10% glycerol, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13B111
SYNCHROTRONSPring-8 BL12B221
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 25, 2011
ADSC QUANTUM 4r2CCDOct 30, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 8038 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.049
Reflection shellResolution: 2.2→2.3 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NOC

3noc


Resolution: 2.2→30 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.233 831 RANDOM
Rwork0.211 --
all0.215 8038 -
obs0.215 7810 -
Solvent computationBsol: 67.432 Å2
Displacement parametersBiso max: 134.65 Å2 / Biso mean: 36.5881 Å2 / Biso min: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1--13.638 Å20 Å2-3.05 Å2
2--13.037 Å20 Å2
3---0.601 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 0 34 1216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.95
LS refinement shellResolution: 2.2→2.3 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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